Mercurial > repos > greg > ideas_genome_tracks
changeset 22:a3740127fc5e draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 20 Nov 2017 14:48:31 -0500 |
| parents | 5201e615dd7f |
| children | 048a6d8d26a8 |
| files | ideas_genome_tracks.R |
| diffstat | 1 files changed, 41 insertions(+), 26 deletions(-) [+] |
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--- a/ideas_genome_tracks.R Mon Nov 20 14:48:21 2017 -0500 +++ b/ideas_genome_tracks.R Mon Nov 20 14:48:31 2017 -0500 @@ -40,22 +40,36 @@ return(state_color); } +get_hue = function(val, min=0, max=1) { + if (is.null(val)) { + val = max; + } else if (is.na(val)) { + val = max; + } else if (val < min) { + val = min; + } else if (val > max) { + val = max; + } + return(val); +} + get_track_file_name = function(base_track_file_name, index, ext) { track_file_name <- paste(base_track_file_name, index, ext, sep="."); return(track_file_name); } -get_state_color = function(statemean, markcolor=NULL) -{ +get_state_color = function(statemean, markcolor=NULL) { + sm_width = dim(statemean)[1]; + sm_height = dim(statemean)[2]; if (length(markcolor) == 0) { - markcolor = rep("", dim(statemean)[2]); - markcolor[order(apply(statemean, 2, sd), decreasing=T)] = hsv((1:dim(statemean)[2]-1)/dim(statemean)[2], 1, 1); + markcolor = rep("", sm_height); + markcolor[order(apply(statemean, 2, sd), decreasing=T)] = hsv((1:sm_height-1)/sm_height, 1, 1); markcolor = t(col2rgb(markcolor)); } rg = apply(statemean, 1, range); mm = NULL; - for(i in 1:dim(statemean)[1]) { - mm = rbind(mm, (statemean[i,]-rg[1,i])+1e-10)/(rg[2,i]-rg[1,i]+1e-10)); + for (i in 1:sm_width) { + mm = rbind(mm, statemean[i,] - rg[1,i] + 1e-10 / rg[2,i] - rg[1,i] + 1e-10); } mm = mm^6; if(dim(mm)[2] > 1) { @@ -64,7 +78,7 @@ mycol = mm%*%markcolor; s = apply(statemean, 1, max); s = (s - min(s)) / (max(s) - min(s) + 1e-10); - h = t(apply(mycol, 1, function(x) {rgb2hsv(x[1], x[2], x[3])})); + h = t(apply(mycol, 1, function(x) {rgb2hsv(r=get_hue(x[1]), g=get_hue(x[2]), b=get_hue(x[3]))})); h[,2] = h[,2] * s; h = apply(h, 1, function(x) {hsv(x[1], x[2], x[3])}); rt = cbind(apply(t(col2rgb(h)), 1, function(x) {paste(x, collapse=",")}), h); @@ -72,15 +86,14 @@ } create_primary_html = function(output_trackhub, tracks_dir) { - track_files <- list.files(path=tracks_dir, full.names=TRUE); - s <- "<html><head></head><body><ul>" + track_files <- list.files(path=tracks_dir); + s <- paste('<html>\n<head>\n</head>\n<body>\n<ul>\n', sep=""); for (i in 1:length(track_files)) { - track_file <- track_files[i]; - s <- paste(s, "<li><a href=\"", track_file, "\">", track_file, "</a></li>"); - s <- paste(s, "</ul></body></html>" - sink(output_trackhub); - cat(s); - sink(); + track_file <- paste("tracks", track_files[i], sep="/"); + s <- paste(s, '<li>\n<a href="', track_file, '">', track_file, '</a>\n</li>', sep=""); + } + s <- paste(s, '</ul>\n</body>\n</html>', sep=""); + cat(s, file=output_trackhub); } create_track = function(input_dir_state, chrom_len_file, base_track_file_name, state_color) { @@ -148,7 +161,7 @@ track_db = NULL; for(i in 1:length(cells)) { - ii = which(cells[i] == cellinfo[,1]); + ii = which(cells[i] == cell_info[,1]); if (length(ii) == 0) { next; } @@ -156,13 +169,13 @@ # trackDb.txt track entry. track_db = c(track_db, paste(hub_name, "_track_", i, sep="")); track_db = c(track_db, "type bigBed"); - track_db = c(track_db, paste("bigDataUrl ", get_track_file_name(base_track_file_name, i, "bigbed")); - track_db = c(track_db, paste("shortLabel", short_label)); - track_db = c(track_db, paste("longLabel", long_label); - track_db = c(track_db, paste("priority", i)); + track_db = c(track_db, paste("bigDataUrl", get_track_file_name(base_track_file_name, i, "bigbed"), sep=" ")); + track_db = c(track_db, paste("shortLabel", short_label, sep=" ")); + track_db = c(track_db, paste("longLabel", long_label, sep=" ")); + track_db = c(track_db, paste("priority", ii)); track_db = c(track_db, "itemRgb on"); track_db = c(track_db, "maxItems 100000"); - track_db = c(track_db, paste("color", paste(c(col2rgb(cellinfo[ii,4])), collapse=","))); + track_db = c(track_db, paste("color", paste(c(col2rgb(cell_info[ii,4])), collapse=","), sep=" ")); track_db = c(track_db, "visibility dense"); track_db = c(track_db, ""); } @@ -173,13 +186,15 @@ state_color <- create_color_scheme(opt$input_dir_para); # Create the hub.txt output. -contents <- c(paste("hub", opt$hub_name), paste("shortLabel",opt$short_label), paste("longLabel", opt$long_label), paste("genomesFile genomes.txt", sep=""), paste("email", opt$email)) -hub_file_path <- paste(opt$output_trackhub_files_path, "/", "hub.txt", sep="") +contents <- c(paste("hub", opt$hub_name), paste("shortLabel",opt$short_label), paste("longLabel", opt$long_label), paste("genomesFile genomes.txt", sep=""), paste("email", opt$email)); +hub_dir <- paste(opt$output_trackhub_files_path, "/", "myHub", "/", sep=""); +dir.create(hub_dir, showWarnings=FALSE); +hub_file_path <- paste(hub_dir, "hub.txt", sep="/"); write.table(contents, file=hub_file_path, quote=F, row.names=F, col.names=F); # Create the genomes.txt output. -contents <- c(paste("genome", opt$build), paste("trackDb ", opt$build, "/", "trackDb.txt", sep="")) -genomes_file_path <- paste(opt$output_trackhub_files_path, "/", "genomes.txt", sep="") +contents <- c(paste("genome", opt$build), paste("trackDb ", opt$build, "/", "trackDb.txt", sep="")); +genomes_file_path <- paste(opt$output_trackhub_files_path, "/", "genomes.txt", sep=""); write.table(contents, file=genomes_file_path, quote=F, row.names=F, col.names=F); # Create the tracks. @@ -188,7 +203,7 @@ track_db <- create_track_db(opt$input_dir_state, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$short_label, opt$long_label, state_color); # Create the trackDb.txt output. -track_db_file_path <- paste(tracks_dir, "/", paste("trackDb.txt", sep=""), sep="") +track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep=""); write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F); # Create the primary HTML dataset.